RetrogeneDB ID: retro_ocun_456

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:72223804..72224487(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008407
• Aliases: None
• Description: None

Sequence

>retro_ocun_456
AGAAAGTGGAGGAATGTCGCAGAGCTAAAGATCGAGTGCCTGAGGAAGAAGTTTGCCCGAAAGATGCTTGGAAAGACGAG
GAGGAAGCTTATGTGTGAAACAGCCGAGCGCTCTCGCAGGGAACACAGGCGGACGCACAGCGCTGATACTCGTAAGCGAG
GCTGGCAAGAGAAGCTGGCGACTTCCGCGAGCCTGCAGAACCCACGTTGGCACGCGTCCCCAGGATCCGAGGTATCAGTG
GTACGAGCCCCAGAGCCCGAAAAGCATCGCAGCTTCCTCGCCTTCGCCAGCTCTTCAGCGGCACCCTTGGAAAGCGCAGC
AAGGCTCGATGAACACGCTGAGGACTGCGGAACCATATATCGCCCGCGGGCACCCGAATCTGAAGTCAGTACATGAAGTA
ATTTACAAGCGTGGCTGTGGCAAGTCAATAAGAAGCGAACTGGCTTGACTGATAGCCCTCTGACGGCCCGTTCTCTTGGT
AAATCCAGTATCATCTGCATGGAGGATCGGATTCACGCAGTCTATACTGCCGGAAAACGCCTCAAGGAAGCAATCAACTT
CCTGTGGCCCTTCAAGTCATCTTCTCTCCGAGGTGGGATGCAGCAAAAGACCACCCATTTTGTAGACGGTGGAGATGCAG
GCAACAGGGAAGACCAATCGGCAGACCTATCAGAAGGACGAAC

Alignment

ORF - retro_ocun_456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.81 %
• Parental protein coverage: 91.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRM-ARMARKAGNFYVPAEPK
          .K.RN.AELKI..LRKKFA.KML.K.RRKL..E.A.....E.R.......R..AR.AR.AG.F..PAEP.
Retrocopy RKWRNVAELKIECLRKKFARKMLGKTRRKLMCETAERSRREHRRTHSADTRK<ARLAREAGDFREPAEPT

Parental  LAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKA-SINMLRIVEPYIAWGYPNLKSVNELIYKR
          LA.V.RIRGI.G.SP..RK..QL.RLRQ.F.GT..K..KA.S.N.LR..EPYIA.G.PNLKSV.E.IYKR
Retrocopy LARVPRIRGISGTSPRARKASQLPRLRQLFSGTLGKRSKA<SMNTLRTAEPYIARGHPNLKSVHEVIYKR

Parental  GYGK-INKKRIALTDNTLIARSLGKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTH
          G.GK..NKKR..LTD..L.ARSLGK..IICMED.IH..YT.GK..KEA.NFLWPFK.SS.RGGM..KTTH
Retrocopy GCGK<VNKKRTGLTDSPLTARSLGKSSIICMEDRIHAVYTAGKRLKEAINFLWPFKSSSLRGGMQQKTTH

Parental  FVEGGDAGNREDQ-INRLIRRMN
          FV.GGDAGNREDQ.I.R.IRR.N
Retrocopy FVDGGDAGNREDQ<IGRPIRRTN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	179.03 RPM
SRP017611_kidney	0.20 RPM	399.55 RPM
SRP017611_liver	0.00 RPM	123.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_456 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_456 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000003844	6 retrocopies	retro_ocun_1393, retro_ocun_1604, retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456 , retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287, retro_pvam_308, retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,